PT  - JOURNAL ARTICLE
AU  - Schmidt, Henri
AU  - Zhang, Minsi
AU  - Mourelatos, Haralambos
AU  - Sánchez-Rivera, Francisco J.
AU  - Lowe, Scott W.
AU  - Ventura, Andrea
AU  - Leslie, Christina S.
AU  - Pritykin, Yuri
TI  - Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2
AID  - 10.1101/2022.05.02.490368
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.05.02.490368
4099  - http://biorxiv.org/content/early/2022/05/03/2022.05.02.490368.short
4100  - http://biorxiv.org/content/early/2022/05/03/2022.05.02.490368.full
AB  - We present GuideScan2 for memory-efficient, parallelizable construction of high-specificity CRISPR guide RNA (gRNA) databases and user-friendly gRNA/library design in custom genomes. GuideScan2 analysis identified widespread confounding effects of low-specificity gRNAs in published CRISPR knockout, interference and activation screens and enabled construction of a ready-to-use gRNA library that reduced off-target effects in a novel gene essentiality screen. GuideScan2 also enabled the design and experimental validation of allele-specific gRNAs in a hybrid mouse genome.Competing Interest StatementS.W.L. is an advisor for and has equity in the following biotechnology companies: ORIC Pharmaceuticals, Faeth Therapeutics, Blueprint Medicines, Geras Bio, Mirimus Inc. and PMV Pharmaceuticals. S.W.L. acknowledges receiving funding and research support from Agilent Technologies for the purposes of massively parallel oligo synthesis.